FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: 52MNZ

Calculation Name: 1NXM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1NXM

Chain ID: A

ChEMBL ID:

UniProt ID: Q8GIQ0

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 194
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2231202.892285
FMO2-HF: Nuclear repulsion 2155081.208193
FMO2-HF: Total energy -76121.684093
FMO2-MP2: Total energy -76349.132376


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:4:ASN)


Summations of interaction energy for fragment #1(A:4:ASN)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-7.268-3.7931.196-1.852-2.8170.011
Interaction energy analysis for fragmet #1(A:4:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.019 / q_NPA : -0.029
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A6PHE00.0290.0053.867-1.7670.200-0.023-1.002-0.941-0.002
4A7GLY0-0.027-0.0155.0161.3381.404-0.001-0.002-0.0620.000
5A8LYS10.7770.9122.460-7.072-5.6741.221-0.846-1.7730.013
6A9THR00.000-0.0146.751-0.868-0.8680.0000.0000.0000.000
7A10LEU0-0.0150.0038.6760.2010.2010.0000.0000.0000.000
8A11ALA0-0.009-0.0039.100-0.139-0.1390.0000.0000.0000.000
9A12ALA00.0230.01010.977-0.045-0.0450.0000.0000.0000.000
10A13ARG10.7850.8635.661-0.090-0.0900.0000.0000.0000.000
11A14PRO00.0150.00212.088-0.094-0.0940.0000.0000.0000.000
12A15VAL0-0.0040.00712.884-0.059-0.0590.0000.0000.0000.000
13A16GLU-1-0.956-0.97815.252-0.304-0.3040.0000.0000.0000.000
14A17ALA00.0090.01417.4930.0340.0340.0000.0000.0000.000
15A18ILE00.0060.00218.3360.0250.0250.0000.0000.0000.000
16A19PRO00.0330.01819.7190.0260.0260.0000.0000.0000.000
17A20GLY00.0160.00420.5940.0060.0060.0000.0000.0000.000
18A21MET00.0040.01415.5120.0050.0050.0000.0000.0000.000
19A22LEU0-0.043-0.00914.7510.0050.0050.0000.0000.0000.000
20A23GLU-1-0.725-0.8247.339-1.601-1.6010.0000.0000.0000.000
21A24PHE00.014-0.01410.5710.1270.1270.0000.0000.0000.000
22A25ASP-1-0.816-0.8725.1342.2112.255-0.001-0.002-0.0410.000
23A26ILE0-0.008-0.0237.929-0.102-0.1020.0000.0000.0000.000
24A27PRO0-0.011-0.0088.4530.3800.3800.0000.0000.0000.000
25A28VAL0-0.0080.0118.325-0.460-0.4600.0000.0000.0000.000
26A29HIS0-0.004-0.0019.0980.6270.6270.0000.0000.0000.000
27A30GLY00.029-0.00511.336-0.306-0.3060.0000.0000.0000.000
28A31ASP-1-0.778-0.85310.2401.0951.0950.0000.0000.0000.000
29A32ASN00.003-0.01310.596-0.055-0.0550.0000.0000.0000.000
30A33ARG10.7900.85811.844-0.754-0.7540.0000.0000.0000.000
31A34GLY00.0020.00914.136-0.096-0.0960.0000.0000.0000.000
32A35TRP0-0.030-0.01411.7690.1880.1880.0000.0000.0000.000
33A36PHE0-0.0080.00014.120-0.124-0.1240.0000.0000.0000.000
34A37LYS10.8210.88612.512-0.254-0.2540.0000.0000.0000.000
35A38GLU-1-0.879-0.95014.6430.6050.6050.0000.0000.0000.000
36A39ASN0-0.027-0.01614.8890.0690.0690.0000.0000.0000.000
37A40PHE00.0490.01415.910-0.046-0.0460.0000.0000.0000.000
38A41GLN0-0.022-0.01517.941-0.032-0.0320.0000.0000.0000.000
39A42LYS10.8540.91819.636-0.166-0.1660.0000.0000.0000.000
40A43GLU-1-0.865-0.91622.1710.4620.4620.0000.0000.0000.000
41A44LYS10.8280.90517.714-0.628-0.6280.0000.0000.0000.000
42A45MET0-0.0250.00816.1360.0480.0480.0000.0000.0000.000
43A46LEU0-0.0260.00318.686-0.031-0.0310.0000.0000.0000.000
44A47PRO0-0.032-0.02020.082-0.028-0.0280.0000.0000.0000.000
45A48LEU0-0.058-0.01514.1600.0090.0090.0000.0000.0000.000
46A49GLY00.0190.01217.003-0.024-0.0240.0000.0000.0000.000
47A50PHE0-0.019-0.00618.186-0.050-0.0500.0000.0000.0000.000
48A51PRO00.0140.01820.1100.0120.0120.0000.0000.0000.000
49A52GLU-1-0.722-0.86923.5860.1560.1560.0000.0000.0000.000
50A53SER0-0.022-0.01426.535-0.003-0.0030.0000.0000.0000.000
51A54PHE0-0.035-0.01023.695-0.011-0.0110.0000.0000.0000.000
52A55PHE00.040-0.01123.9950.0010.0010.0000.0000.0000.000
53A56ALA0-0.031-0.00528.9200.0020.0020.0000.0000.0000.000
54A57GLU-1-0.842-0.91032.0250.0100.0100.0000.0000.0000.000
55A58GLY0-0.060-0.03132.429-0.002-0.0020.0000.0000.0000.000
56A59LYS10.7460.87231.4860.0020.0020.0000.0000.0000.000
57A60LEU0-0.016-0.01125.7720.0100.0100.0000.0000.0000.000
58A61GLN0-0.022-0.01127.7590.0020.0020.0000.0000.0000.000
59A62ASN0-0.073-0.05022.6690.0200.0200.0000.0000.0000.000
60A63ASN00.0270.03524.5400.0160.0160.0000.0000.0000.000
61A64VAL00.003-0.01522.374-0.001-0.0010.0000.0000.0000.000
62A65SER0-0.022-0.01022.1480.0010.0010.0000.0000.0000.000
63A66PHE00.0090.00620.685-0.028-0.0280.0000.0000.0000.000
64A67SER0-0.049-0.03021.575-0.001-0.0010.0000.0000.0000.000
65A68ARG10.8780.92921.0820.2460.2460.0000.0000.0000.000
66A69LYS10.8770.90917.5900.5730.5730.0000.0000.0000.000
67A70ASN0-0.0180.00020.0280.0010.0010.0000.0000.0000.000
68A71VAL0-0.0420.00021.7110.0060.0060.0000.0000.0000.000
69A72LEU00.0050.00921.156-0.056-0.0560.0000.0000.0000.000
70A73ARG10.7910.89822.2330.3440.3440.0000.0000.0000.000
71A74GLY00.0250.01522.518-0.038-0.0380.0000.0000.0000.000
72A75LEU0-0.0220.01121.4650.0050.0050.0000.0000.0000.000
73A76HIS0-0.049-0.06124.4940.0300.0300.0000.0000.0000.000
74A77ALA0-0.0080.01524.904-0.009-0.0090.0000.0000.0000.000
75A78GLU-1-0.758-0.84826.362-0.114-0.1140.0000.0000.0000.000
76A79PRO00.0010.00327.9450.0000.0000.0000.0000.0000.000
77A80TRP0-0.055-0.04826.4260.0220.0220.0000.0000.0000.000
78A81ASP-1-0.818-0.88123.661-0.064-0.0640.0000.0000.0000.000
79A82LYS10.8200.88920.8430.1780.1780.0000.0000.0000.000
80A83TYR00.0150.01514.8070.0060.0060.0000.0000.0000.000
81A84ILE0-0.0100.00015.5840.0290.0290.0000.0000.0000.000
82A85SER0-0.002-0.01114.1500.0560.0560.0000.0000.0000.000
83A86VAL00.0200.02213.122-0.056-0.0560.0000.0000.0000.000
84A87ALA0-0.009-0.01214.6590.1280.1280.0000.0000.0000.000
85A88ASP-1-0.802-0.91015.862-0.124-0.1240.0000.0000.0000.000
86A89GLY0-0.027-0.02112.3090.0130.0130.0000.0000.0000.000
87A90GLY00.0180.01512.302-0.106-0.1060.0000.0000.0000.000
88A91LYS10.8120.8989.8621.5561.5560.0000.0000.0000.000
89A92VAL00.007-0.00712.2190.1260.1260.0000.0000.0000.000
90A93LEU00.0160.01912.277-0.228-0.2280.0000.0000.0000.000
91A94GLY00.0040.00313.0260.1760.1760.0000.0000.0000.000
92A95THR00.0050.00314.384-0.150-0.1500.0000.0000.0000.000
93A96TRP0-0.040-0.03513.1980.0510.0510.0000.0000.0000.000
94A97VAL00.0500.02119.235-0.037-0.0370.0000.0000.0000.000
95A98ASP-1-0.766-0.83522.300-0.187-0.1870.0000.0000.0000.000
96A99LEU00.0260.02024.0140.0030.0030.0000.0000.0000.000
97A100ARG10.7600.84923.0510.2030.2030.0000.0000.0000.000
98A101GLU-1-0.866-0.94528.944-0.129-0.1290.0000.0000.0000.000
99A102GLY0-0.030-0.03630.2080.0170.0170.0000.0000.0000.000
100A103GLU-1-0.958-0.98128.855-0.150-0.1500.0000.0000.0000.000
101A104THR0-0.022-0.02024.121-0.003-0.0030.0000.0000.0000.000
102A105PHE0-0.047-0.00325.392-0.026-0.0260.0000.0000.0000.000
103A106GLY00.0260.00326.2630.0010.0010.0000.0000.0000.000
104A107ASN0-0.056-0.01921.559-0.035-0.0350.0000.0000.0000.000
105A108THR0-0.044-0.03719.4310.0170.0170.0000.0000.0000.000
106A109TYR0-0.038-0.0429.608-0.023-0.0230.0000.0000.0000.000
107A110GLN00.006-0.01913.9610.0550.0550.0000.0000.0000.000
108A111THR0-0.041-0.0198.462-0.430-0.4300.0000.0000.0000.000
109A112VAL00.0140.0107.5290.2420.2420.0000.0000.0000.000
110A113ILE0-0.0150.0058.153-0.272-0.2720.0000.0000.0000.000
111A114ASP-1-0.771-0.8676.869-1.664-1.6640.0000.0000.0000.000
112A115ALA00.0150.01110.0080.2230.2230.0000.0000.0000.000
113A116SER0-0.009-0.0236.0220.4370.4370.0000.0000.0000.000
114A117LYS10.8180.9085.3943.5893.5890.0000.0000.0000.000
115A118SER0-0.020-0.0148.751-0.066-0.0660.0000.0000.0000.000
116A119ILE00.000-0.00410.813-0.043-0.0430.0000.0000.0000.000
117A120PHE0-0.0160.00113.9780.0370.0370.0000.0000.0000.000
118A121VAL00.002-0.01017.242-0.054-0.0540.0000.0000.0000.000
119A122PRO0-0.0050.00619.5120.0220.0220.0000.0000.0000.000
120A123ARG10.9090.94122.9470.0380.0380.0000.0000.0000.000
121A124GLY0-0.009-0.02026.2720.0020.0020.0000.0000.0000.000
122A125VAL0-0.044-0.02020.349-0.017-0.0170.0000.0000.0000.000
123A126ALA00.0030.00523.6170.0110.0110.0000.0000.0000.000
124A127ASN00.015-0.01219.323-0.053-0.0530.0000.0000.0000.000
125A128GLY00.0380.00519.7310.0460.0460.0000.0000.0000.000
126A129PHE0-0.069-0.02917.036-0.057-0.0570.0000.0000.0000.000
127A130GLN00.0230.00417.195-0.001-0.0010.0000.0000.0000.000
128A131VAL0-0.053-0.02216.506-0.117-0.1170.0000.0000.0000.000
129A132LEU0-0.026-0.00812.351-0.017-0.0170.0000.0000.0000.000
130A133SER0-0.036-0.03213.846-0.048-0.0480.0000.0000.0000.000
131A134ASP-1-0.847-0.92415.645-0.444-0.4440.0000.0000.0000.000
132A135PHE00.008-0.00218.0970.0500.0500.0000.0000.0000.000
133A136VAL00.0010.04315.367-0.058-0.0580.0000.0000.0000.000
134A137ALA00.005-0.00217.6330.0320.0320.0000.0000.0000.000
135A138TYR00.0600.04516.7950.0640.0640.0000.0000.0000.000
136A139SER00.004-0.00518.2580.0350.0350.0000.0000.0000.000
137A140TYR00.0410.03018.5750.0030.0030.0000.0000.0000.000
138A141LEU0-0.0080.01620.6480.0130.0130.0000.0000.0000.000
139A142VAL0-0.013-0.01622.596-0.029-0.0290.0000.0000.0000.000
140A143ASN00.016-0.00825.3840.0050.0050.0000.0000.0000.000
141A144ASP-1-0.799-0.89628.077-0.010-0.0100.0000.0000.0000.000
142A145TYR0-0.031-0.01430.500-0.002-0.0020.0000.0000.0000.000
143A146TRP0-0.012-0.00633.227-0.001-0.0010.0000.0000.0000.000
144A147ALA00.0370.01834.7970.0070.0070.0000.0000.0000.000
145A148LEU0-0.001-0.00437.766-0.008-0.0080.0000.0000.0000.000
146A149GLU-1-0.907-0.97139.242-0.039-0.0390.0000.0000.0000.000
147A150LEU00.0170.00633.677-0.005-0.0050.0000.0000.0000.000
148A151LYS10.9610.99635.4130.0780.0780.0000.0000.0000.000
149A152PRO0-0.080-0.05636.411-0.010-0.0100.0000.0000.0000.000
150A153LYS10.7850.88434.2410.0720.0720.0000.0000.0000.000
151A154TYR0-0.029-0.01830.1360.0020.0020.0000.0000.0000.000
152A155ALA0-0.032-0.00530.0580.0030.0030.0000.0000.0000.000
153A156PHE0-0.021-0.01928.745-0.003-0.0030.0000.0000.0000.000
154A157VAL0-0.0010.00726.1860.0080.0080.0000.0000.0000.000
155A158ASN0-0.049-0.03027.497-0.036-0.0360.0000.0000.0000.000
156A159TYR0-0.026-0.05023.889-0.034-0.0340.0000.0000.0000.000
157A160ALA00.0370.03324.451-0.044-0.0440.0000.0000.0000.000
158A161ASP-1-0.789-0.86326.968-0.298-0.2980.0000.0000.0000.000
159A162PRO0-0.033-0.02026.549-0.024-0.0240.0000.0000.0000.000
160A163SER0-0.133-0.08927.191-0.007-0.0070.0000.0000.0000.000
161A164LEU00.0220.01723.7310.0000.0000.0000.0000.0000.000
162A165ASP-1-0.885-0.93120.672-0.653-0.6530.0000.0000.0000.000
163A166ILE0-0.018-0.00118.941-0.058-0.0580.0000.0000.0000.000
164A167LYS10.8110.89317.9600.6830.6830.0000.0000.0000.000
165A168TRP00.024-0.00517.923-0.081-0.0810.0000.0000.0000.000
166A169GLU-1-0.850-0.93013.523-1.437-1.4370.0000.0000.0000.000
167A170ASN0-0.029-0.02617.4550.0440.0440.0000.0000.0000.000
168A171LEU00.0340.03021.1200.0180.0180.0000.0000.0000.000
169A172GLU-1-0.908-0.95824.056-0.488-0.4880.0000.0000.0000.000
170A173GLU-1-0.920-0.94824.499-0.432-0.4320.0000.0000.0000.000
171A174ALA0-0.028-0.00324.105-0.003-0.0030.0000.0000.0000.000
172A175GLU-1-0.779-0.86524.829-0.238-0.2380.0000.0000.0000.000
173A176VAL00.0210.00925.821-0.017-0.0170.0000.0000.0000.000
174A177SER0-0.076-0.05928.0220.0300.0300.0000.0000.0000.000
175A178GLU-1-0.847-0.94830.630-0.192-0.1920.0000.0000.0000.000
176A179ALA0-0.047-0.01231.9330.0050.0050.0000.0000.0000.000
177A180ASP-1-0.761-0.86727.690-0.268-0.2680.0000.0000.0000.000
178A181GLU-1-0.804-0.88629.756-0.306-0.3060.0000.0000.0000.000
179A182ASN0-0.106-0.05831.6340.0050.0050.0000.0000.0000.000
180A183HIS0-0.0390.00628.6970.0240.0240.0000.0000.0000.000
181A184PRO00.0010.00632.562-0.006-0.0060.0000.0000.0000.000
182A185PHE00.0600.02131.119-0.019-0.0190.0000.0000.0000.000
183A186LEU00.0580.02027.4610.0180.0180.0000.0000.0000.000
184A187LYS10.7710.86430.8420.2130.2130.0000.0000.0000.000
185A188ASP-1-0.844-0.90234.216-0.180-0.1800.0000.0000.0000.000
186A189VAL0-0.038-0.00430.5980.0120.0120.0000.0000.0000.000
187A190LYS10.8220.90033.7230.1250.1250.0000.0000.0000.000
188A191PRO0-0.0030.00531.8420.0000.0000.0000.0000.0000.000
189A192LEU00.0120.02429.2750.0160.0160.0000.0000.0000.000
190A193ARG10.8550.91432.2030.0830.0830.0000.0000.0000.000
191A194LYS10.9300.95230.7040.1060.1060.0000.0000.0000.000
192A195GLU-1-0.800-0.88134.757-0.069-0.0690.0000.0000.0000.000
193A196ASP-1-0.808-0.88233.839-0.091-0.0910.0000.0000.0000.000
194A197LEU0-0.0280.01229.0610.0010.0010.0000.0000.0000.000